At this point, they're probably too far into it to either recast via CGI (he's the lead, so this isn't a "Plummer for Spacey" thing) or scrap the whole film, especially a film they obviously think is their ticket to that sweet, sweet, Spiderman money.
If anything, they'll watch and see what happens with the new Fantastic Beasts movie he's in and, if worse comes to worse, dump the Flash onto HBO Max.